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Development of a D genome specific marker resource for diploid and hexaploid wheat.
BMC Genomics. 2015 Aug 28; 16:646.BG

Abstract

BACKGROUND

Mapping and map-based cloning of genes that control agriculturally and economically important traits remain great challenges for plants with complex highly repetitive genomes such as those within the grass tribe, Triticeae. Mapping limitations in the Triticeae are primarily due to low frequencies of polymorphic gene markers and poor genetic recombination in certain genetic regions. Although the abundance of repetitive sequence may pose common problems in genome analysis and sequence assembly of large and complex genomes, they provide repeat junction markers with random and unbiased distribution throughout chromosomes. Hence, development of a high-throughput mapping technology that combine both gene-based and repeat junction-based markers is needed to generate maps that have better coverage of the entire genome.

RESULTS

In this study, the available genomics resource of the diploid Aegilop tauschii, the D genome donor of bread wheat, were used to develop genome specific markers that can be applied for mapping in modern hexaploid wheat. A NimbleGen array containing both gene-based and repeat junction probe sequences derived from Ae. tauschii was developed and used to map the Chinese Spring nullisomic-tetrasomic lines and deletion bin lines of the D genome chromosomes. Based on these mapping data, we have now anchored 5,171 repeat junction probes and 10,892 gene probes, corresponding to 5,070 gene markers, to the delineated deletion bins of the D genome. The order of the gene-based markers within the deletion bins of the Chinese Spring can be inferred based on their positions on the Ae. tauschii genetic map. Analysis of the probe sequences against the Chinese Spring chromosome sequence assembly database facilitated mapping of the NimbleGen probes to the sequence contigs and allowed assignment or ordering of these sequence contigs within the deletion bins. The accumulated length of anchored sequence contigs is about 155 Mb, representing ~ 3.2 % of the D genome. A specific database was developed to allow user to search or BLAST against the probe sequence information and to directly download PCR primers for mapping specific genetic loci.

CONCLUSIONS

In bread wheat, aneuploid stocks have been extensively used to assign markers linked with genes/traits to chromosomes, chromosome arms, and their specific bins. Through this study, we added thousands of markers to the existing wheat chromosome bin map, representing a significant step forward in providing a resource to navigate the wheat genome. The database website (http://probes.pw.usda.gov/ATRJM/) provides easy access and efficient utilization of the data. The resources developed herein can aid map-based cloning of traits of interest and the sequencing of the D genome of hexaploid wheat.

Authors+Show Affiliations

Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA. Yi.Wang@ars.usda.gov. Department of Plant Sciences, University of California, Davis, CA, 95616, USA. Yi.Wang@ars.usda.gov.Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA. Thomas.Drader@ars.usda.gov.Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA. vijtiwari@ksu.edu. Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. vijtiwari@ksu.edu.Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA. lldong@genetics.ac.cn. Department of Plant Sciences, University of California, Davis, CA, 95616, USA. lldong@genetics.ac.cn.Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA. ajay.kumar.2.@ndsu.edu.Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA. Department of Plant Sciences, University of California, Davis, CA, 95616, USA.Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA. Molecular Breeding and Genomics Technology Laboratory, BioDiagnostics Inc., River Falls, WI, 54022, USA.Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA.Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA. gerard.lazo@ars.usda.gov.Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA. jeff.leonard@oregonstate.edu.Wheat Genetic Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. bsgill@k-state.edu.Cereal Disease Laboratory, USDA-ARS, Minneapolis, MN, 55108, USA. Shahryar.Kianian@ars.usda.gov.Department of Plant Sciences, University of California, Davis, CA, 95616, USA. mcluo@ucdavis.edu.Western Regional Research Center, USDA-ARS, Albany, CA, 94710, USA. yong.gu@ars.usda.gov.

Pub Type(s)

Journal Article
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

26315263

Citation

Wang, Yi, et al. "Development of a D Genome Specific Marker Resource for Diploid and Hexaploid Wheat." BMC Genomics, vol. 16, 2015, p. 646.
Wang Y, Drader T, Tiwari VK, et al. Development of a D genome specific marker resource for diploid and hexaploid wheat. BMC Genomics. 2015;16:646.
Wang, Y., Drader, T., Tiwari, V. K., Dong, L., Kumar, A., Huo, N., Ghavami, F., Iqbal, M. J., Lazo, G. R., Leonard, J., Gill, B. S., Kianian, S. F., Luo, M. C., & Gu, Y. Q. (2015). Development of a D genome specific marker resource for diploid and hexaploid wheat. BMC Genomics, 16, 646. https://doi.org/10.1186/s12864-015-1852-2
Wang Y, et al. Development of a D Genome Specific Marker Resource for Diploid and Hexaploid Wheat. BMC Genomics. 2015 Aug 28;16:646. PubMed PMID: 26315263.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Development of a D genome specific marker resource for diploid and hexaploid wheat. AU - Wang,Yi, AU - Drader,Thomas, AU - Tiwari,Vijay K, AU - Dong,Lingli, AU - Kumar,Ajay, AU - Huo,Naxin, AU - Ghavami,Farhad, AU - Iqbal,M Javed, AU - Lazo,Gerard R, AU - Leonard,Jeff, AU - Gill,Bikram S, AU - Kianian,Shahryar F, AU - Luo,Ming-Cheng, AU - Gu,Yong Q, Y1 - 2015/08/28/ PY - 2015/02/13/received PY - 2015/08/17/accepted PY - 2015/8/29/entrez PY - 2015/9/1/pubmed PY - 2016/5/25/medline SP - 646 EP - 646 JF - BMC genomics JO - BMC Genomics VL - 16 N2 - BACKGROUND: Mapping and map-based cloning of genes that control agriculturally and economically important traits remain great challenges for plants with complex highly repetitive genomes such as those within the grass tribe, Triticeae. Mapping limitations in the Triticeae are primarily due to low frequencies of polymorphic gene markers and poor genetic recombination in certain genetic regions. Although the abundance of repetitive sequence may pose common problems in genome analysis and sequence assembly of large and complex genomes, they provide repeat junction markers with random and unbiased distribution throughout chromosomes. Hence, development of a high-throughput mapping technology that combine both gene-based and repeat junction-based markers is needed to generate maps that have better coverage of the entire genome. RESULTS: In this study, the available genomics resource of the diploid Aegilop tauschii, the D genome donor of bread wheat, were used to develop genome specific markers that can be applied for mapping in modern hexaploid wheat. A NimbleGen array containing both gene-based and repeat junction probe sequences derived from Ae. tauschii was developed and used to map the Chinese Spring nullisomic-tetrasomic lines and deletion bin lines of the D genome chromosomes. Based on these mapping data, we have now anchored 5,171 repeat junction probes and 10,892 gene probes, corresponding to 5,070 gene markers, to the delineated deletion bins of the D genome. The order of the gene-based markers within the deletion bins of the Chinese Spring can be inferred based on their positions on the Ae. tauschii genetic map. Analysis of the probe sequences against the Chinese Spring chromosome sequence assembly database facilitated mapping of the NimbleGen probes to the sequence contigs and allowed assignment or ordering of these sequence contigs within the deletion bins. The accumulated length of anchored sequence contigs is about 155 Mb, representing ~ 3.2 % of the D genome. A specific database was developed to allow user to search or BLAST against the probe sequence information and to directly download PCR primers for mapping specific genetic loci. CONCLUSIONS: In bread wheat, aneuploid stocks have been extensively used to assign markers linked with genes/traits to chromosomes, chromosome arms, and their specific bins. Through this study, we added thousands of markers to the existing wheat chromosome bin map, representing a significant step forward in providing a resource to navigate the wheat genome. The database website (http://probes.pw.usda.gov/ATRJM/) provides easy access and efficient utilization of the data. The resources developed herein can aid map-based cloning of traits of interest and the sequencing of the D genome of hexaploid wheat. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/26315263/Development_of_a_D_genome_specific_marker_resource_for_diploid_and_hexaploid_wheat_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1852-2 DB - PRIME DP - Unbound Medicine ER -